2018
Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences
Roychowdhury T, Singh VK, Bhattacharya A. Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences. Genomics 2018, 111: 205-211. PMID: 29432978, DOI: 10.1016/j.ygeno.2018.02.004.Peer-Reviewed Original ResearchMeSH KeywordsDNA Barcoding, TaxonomicGenome, BacterialMycobacterium tuberculosisPhylogenyPolymorphism, Single NucleotideVirulenceWhole Genome SequencingConceptsIntra-species genomic variationsPathogenic microbesClassification of organismsWhole genome sequencesContext-specific mannerGenome sequencePhenotypic diversityGenomic variationSingle nucleotide polymorphismsMolecular markersNGS technologiesEscherichia coliNucleotide polymorphismsSpecific mannerE. coliSNPsPathogen classificationMicrobesOrganismsWealth of dataColiMinimal setImportant rolePhylogroupsDiversity
2017
Complex multifractal nature in Mycobacterium tuberculosis genome
Mandal S, Roychowdhury T, Chirom K, Bhattacharya A, Brojen Singh RK. Complex multifractal nature in Mycobacterium tuberculosis genome. Scientific Reports 2017, 7: 46395. PMID: 28440326, PMCID: PMC5404331, DOI: 10.1038/srep46395.Peer-Reviewed Original ResearchMeSH KeywordsDrug Resistance, Multiple, BacterialGenetic VariationGenome, BacterialMicrobial Sensitivity TestsMycobacterium tuberculosis
2015
Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis
Roychowdhury T, Mandal S, Bhattacharya A. Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Scientific Reports 2015, 5: 12567. PMID: 26215170, PMCID: PMC4517164, DOI: 10.1038/srep12567.Peer-Reviewed Original ResearchConceptsDifferent lineagesGenome-level variationCopy number patternsNext-generation sequencing platformsGenome evolutionUseful molecular markerAncestral insertionIndependent evolutionPhylogenetic treeGenome sequenceMycobacterium tuberculosis genomeInsertion siteSequencing platformsMolecular markersComputational pipelineRecombinational lossLineagesIS6110 insertion sitesTuberculosis genomeDifferent isolatesNGS dataInsertion regionInsertion data
2013
Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data
Roychowdhury T, Vishnoi A, Bhattacharya A. Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data. Scientific Reports 2013, 3: 2634. PMID: 24022334, PMCID: PMC3769656, DOI: 10.1038/srep02634.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputational BiologyEscherichia coliGenomeGenomicsHigh-Throughput Nucleotide SequencingHumansMycobacterium tuberculosisPhylogenySequence Analysis, DNAVibrio choleraeConceptsPhylogenetic analysisNext-generation sequencing datasetsWhole genome sequencesNGS dataNext-generation sequencing dataEvolutionary relationshipsStrains/isolatesPhylogenetic constructionDistinct lineagesReference genomeGenome sequenceSequencing datasetsSequencing dataEscherichia coliPhylogenyDifferent strainsVibrio choleraBootstrap analysisGenomeLineagesOrganismsColiInner branchesUnprecedented scalePathogensGenetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients
Das S, Roychowdhury T, Kumar P, Kumar A, Kalra P, Singh J, Singh S, Prasad H, Bhattacharya A. Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients. BMC Genomics 2013, 14: 404. PMID: 23773324, PMCID: PMC3699378, DOI: 10.1186/1471-2164-14-404.Peer-Reviewed Original ResearchConceptsM. tuberculosisClinical isolatesDrug resistant tubercle bacilliExtra-pulmonary tuberculosis patientsMajor public health problemExtra-pulmonary patientsNon-pulmonary sitesResistant tubercle bacilliExtra-pulmonary TBExtra-pulmonary tuberculosisPublic health problemSingle nucleotide variationsSpread of tuberculosisTotal clinical casesNext-generation sequencing approachHIV patientsImmunocompetent patientsTuberculosis patientsClinical manifestationsPulmonary patientsM. tuberculosis H37RvPatient isolatesCerebrospinal fluidHealth problemsPatients